Previous changeset 16:798da6bdff3d (2022-02-22) Next changeset 18:83aac7741200 (2024-07-04) |
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit eeeb69463a2037a6ee620b9223cb152fcc39f1b0 |
modified:
preprocessing.xml |
added:
test-data/ComBat_results_Example_processed_file.ibd test-data/ComBat_results_Example_processed_file.imzml test-data/ComBat_results_Example_processed_file.imzml.txt test-data/ComBat_results_Example_processed_file_preprocessing.pdf test-data/Combat_40pixel.ibd test-data/Combat_40pixel.imzML test-data/Example_processed_ComBat_annotation.tabular test-data/annotation_40pixel.tabular test-data/preprocessing_results_combat_40pixel.ibd test-data/preprocessing_results_combat_40pixel.imzml test-data/preprocessing_results_combat_40pixel.imzml.txt test-data/preprocessing_results_combat_40pixel.pdf |
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diff -r 798da6bdff3d -r 611d80c0e29d preprocessing.xml --- a/preprocessing.xml Tue Feb 22 20:56:10 2022 +0000 +++ b/preprocessing.xml Wed Apr 19 22:46:23 2023 +0000 |
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b'@@ -1,4 +1,4 @@\n-<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.0">\n+<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.1">\n <description>\n mass spectrometry imaging preprocessing\n </description>\n@@ -7,7 +7,9 @@\n </macros>\n <expand macro="requirements">\n <requirement type="package" version="2.3">r-gridextra</requirement>\n- <requirement type="package" version="3.3.5">r-ggplot2</requirement>\n+ <requirement type="package" version="3.4.0">r-ggplot2</requirement>\n+ <requirement type="package" version="3.40.0">bioconductor-sva</requirement>\n+ <requirement type="package" version="1.1.0.1">r-randomcolor</requirement>\n </expand>\n <command detect_errors="exit_code">\n <![CDATA[\n@@ -41,6 +43,8 @@\n library(Cardinal)\n library(gridExtra)\n library(ggplot2)\n+library(sva)\n+library(randomcoloR)\n \n \n @READING_MSIDATA_FULLY_COMPATIBLE@\n@@ -448,6 +452,120 @@\n print(plot(msidata, pixel=random_spectra, col="black"))\n title("Spectra after transformation", outer=TRUE, line=0)\n \n+\n+ \n+ \n+ ############################### ComBat batch correction ###########################\n+\n+ #elif str( $method.methods_conditional.preprocessing_method) == \'ComBat_batch_correction\':\n+ print(\'ComBat batch correction of centroided data\')\n+\n+ ## load annotation tabular and define batch and condition column\n+ annotation = read.delim("$method.methods_conditional.annotation_file", header=$method.methods_conditional.feature_header, sep="\\t")\n+ annotation_x = annotation[,$method.methods_conditional.x_column]\n+ annotation_y = annotation[,$method.methods_conditional.y_column]\n+ batch = annotation[,$method.methods_conditional.batch_column]\n+ condition = annotation[,$method.methods_conditional.condition_column]\n+ \n+ ### stop if not enough batches provided\n+ tryCatch(\n+ {\n+\n+ if (unique(batch<2))\n+ {\n+ stop(call.=FALSE)\n+ }\n+ },\n+ error=function(cond) {\n+ ## in case user provided an annotation tabular with less than two batches\n+ message("Error in annotation tabular")\n+ message("Possible problems: Annotation tabular file has not enough batch levels - to perform ComBat at least 2 batches and 2 pixels per batch are necessary)")\n+ stop(call.=FALSE)\n+ }\n+ )\n+ \n+ ## get intensity matrix from imzml file\n+ intensity_matrix = as.matrix(iData(msidata))\n+ mz_names = paste0("mz_", mz(msidata))\n+ pixel_names = paste0("xy_", msidata@elementMetadata@coord@listData[["x"]], "_", msidata@elementMetadata@coord@listData[["y"]])\n+ rownames(intensity_matrix) = mz_names\n+ colnames(intensity_matrix) = pixel_names\n+\n+ ## reorder columns of intensity matrix to row order of batch column\n+ rownames(annotation) = paste0("xy_", annotation_x, "_", annotation_y)\n+ col_order = rownames(annotation)\n+ \n+ ### stop if pixel/sample names (columns) in intensity matrix from imzml file don\'t match samples names (rows) in annotation tabular file \n+ \ttryCatch(\n+ {\n+\n+ if (all(colnames(intensity_matrix) %in% col_order == FALSE))\n+ {\n+ stop(call.=FALSE)\n+ }\n+ },\n+ error=function(cond) {\n+ ## in case pixel names (columns) from the imzml file don\'t match the pixel names in t'..b'e="preprocessing_method" value="ComBat_batch_correction"/>\n+ <param name="annotation_file" value="annotation_40pixel.tabular" ftype="tabular"/>\n+ <param name="feature_header" value="TRUE"/>\n+ <param name="x_column" value="2"/>\n+ <param name="y_column" value="3"/>\n+ <param name="batch_column" value="4"/>\n+ <param name="condition_column" value="6"/>\n+ </conditional>\n+ </repeat>\n+ <output name="QC_overview" file="preprocessing_results_combat_40pixel.pdf" compare="sim_size"/>\n+ <output name="outfile_imzml" ftype="imzml" file="preprocessing_results_combat_40pixel.imzml.txt" compare="sim_size">\n+ <extra_files type="file" file="preprocessing_results_combat_40pixel.imzml" name="imzml" lines_diff="6"/>\n+ <extra_files type="file" file="preprocessing_results_combat_40pixel.ibd" name="ibd" compare="sim_size"/>\n+ </output>\n+ </test>\n+ <test>\n+ <expand macro="processed_infile_imzml"/>\n+ <conditional name="processed_cond">\n+ <param name="processed_file" value="processed"/>\n+ <param name="accuracy" value="50"/>\n+ <param name="units" value="ppm"/>\n+ </conditional>\n+ <repeat name="methods"> \n+ <conditional name="methods_conditional">\n+ <param name="preprocessing_method" value="ComBat_batch_correction"/>\n+ <param name="annotation_file" value="Example_processed_ComBat_annotation.tabular" ftype="tabular"/>\n+ <param name="feature_header" value="TRUE"/>\n+ <param name="x_column" value="2"/>\n+ <param name="y_column" value="3"/>\n+ <param name="batch_column" value="4"/>\n+ <param name="condition_column" value="5"/>\n+ </conditional>\n+ </repeat>\n+ <output name="QC_overview" file="ComBat_results_Example_processed_file_preprocessing.pdf" compare="sim_size"/>\n+ <output name="outfile_imzml" ftype="imzml" file="ComBat_results_Example_processed_file.imzml.txt" compare="sim_size">\n+ <extra_files type="file" file="ComBat_results_Example_processed_file.imzml" name="imzml" lines_diff="6"/>\n+ <extra_files type="file" file="ComBat_results_Example_processed_file.ibd" name="ibd" compare="sim_size"/>\n+ </output>\n+ </test>\n </tests>\n <help>\n <![CDATA[\n@@ -896,6 +1069,20 @@\n - Peak binning: extracts peaks intensities, either peak height or area under curve (from a profile dataset) for a list of m/z (reference) values\n - m/z binning: generates new m/z bins\n - Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems. \n+- ComBat batch correction: corrects the intensity values of picked m/z features according to batches given in an annotation table. For now, it can only be applied to m/z features after peak picking (=centroided data). The annotation table needs to contain the x and y coordinates for each pixel and a batch identifier (e.g. TMA_1, TMA_2, TMA_3). Additionally a condition column can be provided, which is only used for the PCA plots in the pdf file. Example of annotation file for ComBat batch correction:\n+ \n+ ::\n+ \n+ \t x_coord y_coord batch_identifier\tcondition\n+ \t 10 29 TMA_1 A\n+ \t 22 14 TMA_1 B\n+ \t 22 27 TMA_2 A\n+ \t 23 7 TMA_2 B\n+ \t 29 45 TMA_3 A\n+ \t 33 41 TMA_3 B\n+ \t ...\n+ \t ...\n+\n \n \n **Output**\n' |
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diff -r 798da6bdff3d -r 611d80c0e29d test-data/ComBat_results_Example_processed_file.ibd |
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Binary file test-data/ComBat_results_Example_processed_file.ibd has changed |
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diff -r 798da6bdff3d -r 611d80c0e29d test-data/ComBat_results_Example_processed_file.imzml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ComBat_results_Example_processed_file.imzml Wed Apr 19 22:46:23 2023 +0000 |
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diff -r 798da6bdff3d -r 611d80c0e29d test-data/ComBat_results_Example_processed_file.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ComBat_results_Example_processed_file.imzml.txt Wed Apr 19 22:46:23 2023 +0000 |
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@@ -0,0 +1,4 @@ +imzML file: +total 1648 +-rw-r--r-- 1 ubuntu ubuntu 1663576 Feb 15 11:25 ibd +-rw-r--r-- 1 ubuntu ubuntu 18593 Feb 15 11:25 imzml |
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diff -r 798da6bdff3d -r 611d80c0e29d test-data/ComBat_results_Example_processed_file_preprocessing.pdf |
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Binary file test-data/ComBat_results_Example_processed_file_preprocessing.pdf has changed |
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diff -r 798da6bdff3d -r 611d80c0e29d test-data/Combat_40pixel.ibd |
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diff -r 798da6bdff3d -r 611d80c0e29d test-data/Combat_40pixel.imzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Combat_40pixel.imzML Wed Apr 19 22:46:23 2023 +0000 |
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diff -r 798da6bdff3d -r 611d80c0e29d test-data/Example_processed_ComBat_annotation.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Example_processed_ComBat_annotation.tabular Wed Apr 19 22:46:23 2023 +0000 |
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diff -r 798da6bdff3d -r 611d80c0e29d test-data/annotation_40pixel.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotation_40pixel.tabular Wed Apr 19 22:46:23 2023 +0000 |
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diff -r 798da6bdff3d -r 611d80c0e29d test-data/preprocessing_results_combat_40pixel.ibd |
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diff -r 798da6bdff3d -r 611d80c0e29d test-data/preprocessing_results_combat_40pixel.imzml.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/preprocessing_results_combat_40pixel.imzml.txt Wed Apr 19 22:46:23 2023 +0000 |
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@@ -0,0 +1,4 @@ +imzML file: +total 132 +-rw-r--r-- 1 ubuntu ubuntu 63648 Feb 7 17:01 ibd +-rw-r--r-- 1 ubuntu ubuntu 66384 Feb 7 17:01 imzml |
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diff -r 798da6bdff3d -r 611d80c0e29d test-data/preprocessing_results_combat_40pixel.pdf |
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Binary file test-data/preprocessing_results_combat_40pixel.pdf has changed |